basisSelect: Perform basis selection

In JSB-UCLA/scPNMF: scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

Perform basis selection

Description

Wrapper of basis annotation and data-driven basis selection.

Usage

basisSelect(
  W,
  S = NULL,
  X = NULL,
  toTest = TRUE,
  cor_thres = 0.7,
  pval_thres = 0.01,
  return_fig = FALSE,
  adj_method = "BH",
  mc.cores = 10,
  ncol = 4,
  toAnnotate = FALSE,
  dim_use = NULL
)

Arguments

W	The weight matrix output by PNMF
S	The score matrix output by PNMF
X	The input gene by cell logcount matrix
toTest	Whether to select bases by Pearson correlation w/ cell library size and test of multimodality
cor_thres	Pearson correlation w/ cell library size cutoff. Default is 0.7.
pval_thres	Adjusted p-value cutoff on test of multimodality. Default is 0.01.
return_fig	Whether to print scatter plot of score vector against cell library size and distribution of score vectors for each basis.
adj_method	P-value correction method. Default is "BH".
mc.cores	The number of cores to use for function mclapply().
ncol	Columns for facets in plots.
toAnnotate	Whether to perform Gene Ontology (GO) enrichment analysis on each basis
dim_use	The bases (columns) to be used in the selected weight matrix, NULL value uses all bases

Value

The selected weight matrix

JSB-UCLA/scPNMF documentation built on July 19, 2023, 10:28 p.m.